User: andres.firrincieli

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Posts by andres.firrincieli

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Removal of batch effects from RNA-seq data for WGCNA
... For a binary matrix you should use only 1 and 0 instead of 1 and 2. ...
written 25 days ago by andres.firrincieli30
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Comment: C: Removal of batch effects from RNA-seq data for WGCNA
... > On performing WGCNA, I obtained 12 modules with one single module > containing almost half of the genes in analysis. A few forum post > suggested that this might be due to presence of strong driver of > variation (ref1). As the known source of batch was correctly removed, > I wanted ...
written 25 days ago by andres.firrincieli30
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Comment: C: Breaking down the output from plotEigengeneNetworks()
... > What do you mean by KDiff? The function [intramodularConnectivity()][1] calculate the connectivity of nodes to other nodes within the same module (kWithin), outside the module (kOut) and the overall connectivity within the network (kTot). The function also return the kDiff (kWithin - kOut); in ...
written 6 weeks ago by andres.firrincieli30
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Comment: C: Breaking down the output from plotEigengeneNetworks()
... 200 conditions per sample? Could you elaborates because this is getting 'weird'? For me a 'noisy' module is: 1) a module whose expression profile does not agree with the experimental design; 2) a module where every gene/transcript has negative kDiff, i.e., KOut>KIn. For a fast screening I look a ...
written 6 weeks ago by andres.firrincieli30
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Comment: C: Breaking down the output from plotEigengeneNetworks()
... With only two traits and an absurdly high number of modules,269, I suspect that most of the modules are just noise. Therefore, before you proceed with the analysis I would increase the minimum module size to 100 and use a cutHeight of 0.95 when you call the function cutreeDynamic(). Also, did you ...
written 6 weeks ago by andres.firrincieli30
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Comment: C: Subset WGCNA results for export to Cytoscape
... I wasn't able to replicate your error, but I might have an alternitive solution: module = "green" datexpr_green = datExpr[moduleColors == module,moduleColors == module] TOM_green = TOMsimilarityFromExpr(datexpr_green, power = 18, networkType = "signed", TOMType="signed"); probes = n ...
written 10 weeks ago by andres.firrincieli30
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Comment: C: Extracting VST matrix with batch effects removed
... Hi, have a look at this post: [https://support.bioconductor.org/p/62954/][1] [1]: https://support.bioconductor.org/p/62954/ ...
written 10 weeks ago by andres.firrincieli30
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Comment: C: Subset WGCNA results for export to Cytoscape
... Hi Charles, I have encountered this problem before. Can you give me the the results of `dim(datExpr)` and `dim(TOM)`? ...
written 10 weeks ago by andres.firrincieli30
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Comment: C: WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for
... > 1) According to the tutorial recommendations I would need to choose a > soft thresholding power of 3, since it reaches already R^2 of 0.8 and > is also the maximum. However, the power recommendations in the table > of the FAQs suggest a power of 6-12 for my sample size. What would you ...
written 12 weeks ago by andres.firrincieli30
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Comment: C: WGCNA: correlations module-traits, and module membership-gene significance
... For trait 6 I do not see anything wrong. None of the hub genes (genes with the highest module membership) in the turquoise module show a strong correlation with the trait 6. Also, the majority of the genes in the turquoise module show a correlation (pearson) < 0.1 with that trait: geneTrai ...
written 12 weeks ago by andres.firrincieli30

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